The reported beneficial effects of boron on mineralized tissues in animals and humans vary. Thus, a study was performed to assess whether the variability was the result of different forms of boron supplementation, method of supplementation, and increased adiposity of the rabbit experimental model. Thirty-one female New Zealand White rabbits, (aged 8 months, 2–2.5 kg weight) were fed a grain-based high energy diet containing 11.76 MJ/kg (2850 kcal/kg) and 3.88 mg boron/kg. The rabbits were randomly divided into four treatment groups: Control group was not supplemented with boron (n:7; C), and three groups supplemented with 30 mg boron/L in drinking water in the forms of borax decahydrate (Na2O4B7 10H2O, n:10; BD), borax anhydrous (Na2O4B7, n:7; Bah) or boric acid (H2BO3, n:7; BA). Cone beam micro computed tomographic (micro-CT), histological and elemental analysis was used to evaluate the bones/teeth. Results of the experiments demonstrated that boron supplementation had beneficial effects on mineralized tissue but varied with the type of treatment. Mineral density of the femur was increased by the Bah and BA treatments (p < 0.001), but only BA increased mineral density in the tibia (p = 0.015). In incisor teeth, mineral density of dentin was increased by all boron treatments (p < 0.001), and mineral density of enamel was increased by the BD and Bah treatments. Mineral analysis found that all boron treatments increased the boron concentration in tibia and femur. In the tibia, both the BD and Bah treatments decreased the iron concentration, and the BD treatment decreased the magnesium concentration. Sodium and zinc concentrations in the tibia were decreased by the Bah and BA treatments. The boron treatments did not significantly affect the calcium, copper, molybdenum, potassium phosphorus, and sulfur concentrations. The findings show that boron supplementation can have beneficial effects on mineralized tissues in an animal model with increased adiposity, which is a model of increased inflammatory stress. However, this effect varies with the form of boron supplemented, the method of supplementation, and the mineralized tissue examined.